comparison jbrowse2.py @ 64:497fd2d27aa2 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976-dirty

63:ac00dcfb5d1d

                    self.config_json["assemblies"].append(asstrack)
                else:
                    self.config_json["assemblies"] = [
                        asstrack,
                    ]
        url = "%s.paf" % (trackData["label"])
        dest = "%s/%s" % (self.outdir, url)
        self.symlink_or_copy(os.path.realpath(data), dest)
        trackDict = {
            "type": "SyntenyTrack",
            "trackId": tId,

            "adapter": {
                "type": "PAFAdapter",
                "pafLocation": {"uri": url},
                "assemblyNames": passnames,
            },
        }
        style_json = {
            "displays": [
                {
                    "type": "LinearBasicDisplay",
                    "displayId": "%s-LinearBasicyDisplay" % trackDict["trackId"],
                }
            ]
        }
        trackDict["style"] = style_json
        self.tracksToAdd[trackData["assemblyNames"]].append(trackDict)

64:497fd2d27aa2

                    self.config_json["assemblies"].append(asstrack)
                else:
                    self.config_json["assemblies"] = [
                        asstrack,
                    ]
        lab = trackData["label"]
        url = "%s.paf" % (lab)
        dest = "%s/%s" % (self.outdir, url)
        self.symlink_or_copy(os.path.realpath(data), dest)
        trackDict = {
            "type": "SyntenyTrack",
            "trackId": tId,

            "adapter": {
                "type": "PAFAdapter",
                "pafLocation": {"uri": url},
                "assemblyNames": passnames,
            },
            "displays": [
                {"type": "DotplotDisplay", "displayId": "%s-DotplotDisplay" % lab},
                {
                    "type": "LinearComparativeDisplay",
                    "displayId": "%s-LinearComparativeDisplay" % lab,
                },
                {
                    "type": "LinearSyntenyDisplay",
                    "displayId": "%s-LinearSyntenyDisplay" % lab,
                },
                {
                    "type": "LGVSyntenyDisplay",
                    "displayId": "%s-LGVSyntenyDisplay" % lab,
                },
            ],
        }
        style_json = {
            "displays": [
                {
                    "type": "SyntenyDisplay",
                    "displayId": "%s-SyntenyDisplay" % lab,
                }
            ]
        }
        trackDict["style"] = style_json
        self.tracksToAdd[trackData["assemblyNames"]].append(trackDict)